rs504508

chr13-30090862-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.725 in 152,166 control chromosomes in the GnomAD database, including 40,877 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.72 (40877 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.607

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110262 AN: 152048 Hom.: 40860 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.976

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.840

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.720

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.739

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.725 AC: 110316 AN: 152166 Hom.: 40877 Cov.: 33 AF XY: 0.714 AC XY: 53111 AN XY: 74386

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.678

Gnomad4 ASJ AF: 0.840

Gnomad4 EAS AF: 0.396

Gnomad4 SAS AF: 0.720

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.811

Gnomad4 OTH AF: 0.737

Alfa AF: 0.793 Hom.: 62100

Bravo AF: 0.718

Asia WGS AF: 0.546 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.5
Dann	Benign	0.72

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs504508; hg19: chr13-30664999;